MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : mmcoa__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3399 b4069 b2744 b3708 b3008 b2297 b2458 b1238 b2883 b2797 b3117 b1814 b4471 b1623 b3665 b0411 b3709 b4381 b3161 b0112 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b3035 b2578 b1533 b3927 b3821 b1473 b3447 b4141 b1798 b3662 b1517 b1378   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.706255 (mmol/gDw/h)
  Minimum Production Rate : 0.195400 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.306902
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.995291
  EX_pi_e : 1.267457
  EX_so4_e : 0.373249
  EX_k_e : 0.137856
  EX_fe2_e : 0.011343
  EX_mg2_e : 0.006127
  EX_ca2_e : 0.003676
  EX_cl_e : 0.003676
  EX_cu2_e : 0.000501
  EX_mn2_e : 0.000488
  EX_zn2_e : 0.000241
  EX_ni2_e : 0.000228
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.665397
  EX_co2_e : 24.911764
  EX_h_e : 7.877522
  EX_ac_e : 0.606571
  Auxiliary production reaction : 0.195400
  DM_mththf_c : 0.000316
  DM_5drib_c : 0.000159
  DM_4crsol_c : 0.000157

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

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Last updated: 21-Sep-2023
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